scanScNMT: import an scNMT raw methylation file (chrom, start, %meth)

In trichelab/enmity: load scNMT data and test HDF5/DelayedArray/restfulSE behavior

Description

import an scNMT raw methylation file (chrom, start, %meth)

Usage

scanScNMT(
  tsv,
  dry = FALSE,
  gen = "GRCm38",
  seqinf = FALSE,
  verbose = FALSE,
  which = NULL,
  ...
)

Arguments

tsv	a tsv or tsv.gz filename (will figure out what to do with it)
dry	dry run? (just check that the file is tabixed?) (FALSE)
gen	what genome the file corresponds to (default is GRCm38)
seqinf	add seqInfo? (leave FALSE if running behind a firewall)
verbose	be verbose? (FALSE)
which	optional GRanges to restrict reading of coordinates (NULL)
...	additional arguments to pass on to rtracklayer::import

Value

   a GRanges with appropriate seqinfo and scores turned to betas

trichelab/enmity documentation built on Sept. 8, 2020, 8:32 p.m.